From Online Dictionary of Crystallography

Definition

A three-dimensional description of the electron density in a crystal structure, determined from X-ray diffraction experiments. X-rays scatter from the electron clouds of atoms in the crystal lattice; the diffracted waves from scattering planes h,k,l are described by structure factors The electron density as a function of position x,y,z is the Fourier transform of the structure factors:

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The electron density map describes the contents of the unit cells averaged over the whole crystal and not the contents of a single unit cell (a distinction that is important where structural disorder is present).

Three-dimensional maps are often evaluated as parallel two-dimensional contoured sections at different heights in the unit cell.